Contacts of the strand formed by residues 81 - 89 (chain G) in PDB entry 5HJD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 81 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G TRP* 4.0 16.4 - + - -
55G LEU* 4.1 2.0 - - + -
56G HIS* 3.7 31.6 - + + -
59G PHE* 3.9 25.1 - + - -
79G ALA 3.7 7.6 - - - -
80G GLY* 1.3 79.5 - - - +
82G ILE* 1.3 75.8 + - - +
83G LEU* 3.6 36.4 + - + -
103G ASP* 3.9 0.5 - - - +
104G LEU* 3.0 49.3 + - + +
17L ARG* 3.6 15.7 - - - +
18L KCR 3.6 30.1 - - + +
20L LEU* 5.0 2.9 - - + -
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Residues in contact with ILE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G HIS 4.6 0.5 - - - +
55G LEU 5.8 0.2 - - - -
56G HIS* 6.0 0.2 - - - -
81G PHE* 1.3 81.5 - - - +
83G LEU* 1.3 62.2 + - - +
84G PRO* 3.2 16.3 - - + +
101G ASP* 4.0 33.0 - - + +
102G TYR 3.6 2.2 - - - +
103G ASP* 3.9 28.5 - - + +
17L ARG* 4.0 16.8 - - - +
20L LEU* 5.7 3.8 - - + +
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Residues in contact with LEU 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G TRP* 4.5 0.9 - - + -
34G VAL* 4.1 11.2 - - + -
53G PHE* 3.9 15.9 - - + -
54G HIS 3.6 33.9 - - - +
55G LEU* 3.6 21.5 - - + -
81G PHE* 3.6 20.8 + - + -
82G ILE* 1.3 73.1 - - - +
84G PRO* 1.3 69.7 - - - +
85G ILE* 3.3 16.6 + - + +
102G TYR* 2.6 37.9 + - + +
104G LEU* 3.9 28.7 - - + -
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Residues in contact with PRO 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G HIS* 2.9 63.2 + - + +
82G ILE* 3.2 16.6 - - + +
83G LEU* 1.3 81.3 - - - +
85G ILE* 1.3 59.9 + - - +
86G GLU* 6.0 0.2 - - + -
99G ARG* 3.9 34.5 - - + +
100G PHE 3.4 8.5 - - - +
101G ASP* 4.1 6.1 - - - +
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Residues in contact with ILE 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 4.3 8.1 - - + -
34G VAL* 4.4 8.7 - - + -
35G PHE 5.1 0.2 - - - +
36G VAL* 4.0 19.3 - - + -
51G VAL* 3.7 26.7 - - + -
52G VAL 3.4 5.4 - - - +
53G PHE* 3.8 21.8 - - + -
83G LEU* 3.4 23.1 - - + +
84G PRO* 1.3 75.2 - - - +
86G GLU* 1.3 66.5 + - - +
87G VAL* 4.2 4.7 - - + -
98G VAL 3.8 0.9 - - - +
99G ARG* 3.3 5.4 - - - +
100G PHE* 2.7 43.8 + - + +
102G TYR* 3.8 26.9 - - + -
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Residues in contact with GLU 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G LYS 3.9 0.9 - - - +
51G VAL* 3.4 2.8 - - - -
52G VAL* 2.6 47.0 + - + +
54G HIS* 3.3 28.1 + - + +
84G PRO* 6.0 0.2 - - + -
85G ILE* 1.3 77.0 - - - +
87G VAL* 1.3 63.5 + - - +
88G TYR* 3.2 31.5 + - + -
97G LYS* 3.4 31.7 + - + -
98G VAL 3.4 4.0 - - - +
99G ARG* 4.1 24.4 - - + +
202G SO4 5.2 0.3 + - - -
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Residues in contact with VAL 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G LEU* 4.5 14.1 - - + -
36G VAL* 4.4 22.2 - - + -
48G VAL* 3.9 34.5 - - + -
50G LYS 3.7 2.0 - - - -
51G VAL* 4.4 11.7 - - + +
85G ILE* 4.6 6.5 - - + -
86G GLU* 1.3 75.6 - - - +
88G TYR* 1.3 63.4 + - - +
89G PHE* 3.9 16.3 - - + -
97G LYS* 3.3 3.2 - - - -
98G VAL* 2.9 46.1 + - + +
100G PHE* 4.5 8.7 - - + -
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Residues in contact with TYR 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G VAL* 3.5 7.3 - - - +
49G GLU* 2.6 33.7 + - + -
50G LYS* 2.8 55.9 + - + +
52G VAL* 3.8 21.0 - - + +
86G GLU* 3.2 33.7 + - + -
87G VAL* 1.3 77.3 - - - +
89G PHE* 1.3 58.7 + - - +
96G ARG* 3.7 11.7 - - + +
97G LYS* 3.5 27.2 + - + -
202G SO4 3.2 41.3 + - - -
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Residues in contact with PHE 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G PHE* 3.2 29.6 - + - +
48G VAL* 4.7 0.2 - - + -
49G GLU* 3.7 12.9 - - - +
87G VAL* 3.9 17.5 - - + -
88G TYR* 1.3 78.8 - - - +
90G LYS* 1.3 59.7 + - - +
91G ASN* 2.8 25.7 + - + +
95G PRO* 3.7 18.2 - - + -
96G ARG* 3.1 26.2 + - - +
97G LYS* 3.8 21.1 - - - -
98G VAL* 3.5 26.2 - - + -
122G LEU* 3.7 20.9 - - + -
124G PHE* 3.6 28.3 - + - -
131G PHE* 3.9 9.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il